BigSMILES: A Structurally-Based Line Notation for Describing Macromolecules
BigSMILES: A Structurally-Based Line Notation for Describing Macromolecules
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DOI：
10.1021/acscentsci.9b00476
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发表时间：
2019-09-25
影响因子：
18.2
通讯作者：
Olsen, Bradley D.
中科院分区：
文献类型：
--
作者：
Lin, Tzyy-Shyang;Coley, Connor W.;Olsen, Bradley D.
拥有一个紧凑但结构稳健的识别符或表示系统是在化学界内有效分享和传播研究成果的一个关键促成因素，这种系统为未来的信息学和数据驱动的研究奠定了必要的基础。虽然在小分子方面已经取得了实质性的进展，但聚合物社区在提出有效的表示系统方面一直举步维艰。这是因为，与化学中的其他学科不同，每个不同的化学物种对应于一个明确定义的化学结构的基本前提不适用于聚合物。聚合物本质上是随机的分子，通常是具有分布的化学结构的系综。这一困难限制了为小分子开发的所有确定性表示的适用性。在这项工作中，提出了一种新的表示系统，它能够处理聚合物的随机性质。新系统基于流行的“简化分子输入行输入系统”(SMILES)，其目的是提供可用作聚合物数据库中条目的索引识别符的表示法。作为初步试验，线性聚合物的玻璃化转变温度的标准数据集(Bicerano，2002)的条目被转换成新的BigSMILES语言。此外，希望拟议的系统将为聚合物社区内的交流提供一种更有效的语言，并增加社区内研究人员之间的凝聚力。
Having a compact yet robust structurally based identifier or representation system is a key enabling factor for efficient sharing and dissemination of research results within the chemistry community, and such systems lay down the essential foundations for future informatics and data-driven research. While substantial advances have been made for small molecules, the polymer community has struggled in coming up with an efficient representation system. This is because, unlike other disciplines in chemistry, the basic premise that each distinct chemical species corresponds to a well-defined chemical structure does not hold for polymers. Polymers are intrinsically stochastic molecules that are often ensembles with a distribution of chemical structures. This difficulty limits the applicability of all deterministic representations developed for small molecules. In this work, a new representation system that is capable of handling the stochastic nature of polymers is proposed. The new system is based on the popular "simplified molecular-input line-entry system" (SMILES), and it aims to provide representations that can be used as indexing identifiers for entries in polymer databases. As a pilot test, the entries of the standard data set of the glass transition temperature of linear polymers (Bicerano, 2002) were converted into the new BigSMILES language. Furthermore, it is hoped that the proposed system will provide a more effective language for communication within the polymer community and increase cohesion between the researchers within the community.